replace intake_fetcher by pooch

scivision-gallery · Nov 12, 2023 · 188674d · 188674d
1 parent b7af4a2
commit 188674d
Showing 1 changed file with 48 additions and 5 deletions.
diff --git a/tree-crown-detection.ipynb b/tree-crown-detection.ipynb
@@ -80,7 +80,7 @@
    "source": [
     "from scivision.catalog import default_catalog\n",
     "from scivision.io import load_dataset, load_pretrained_model\n",
-    "from intake_zenodo_fetcher import download_zenodo_files_for_entry"
+    "from pooch"
    ]
   },
   {
@@ -606,16 +606,59 @@
     "target_datasource"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "We use `pooch` to fetch the file from the Zenodo repository."
+   ],
+   "metadata": {
+    "collapsed": false
+   }
+  },
   {
    "cell_type": "code",
    "execution_count": 9,
-   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "Downloading data from 'doi:10.5281/zenodo.5494629/Sep_2014_RGB_602500_646600.tif' to file '/Users/acoca/repo/tree-crown-detection/Sep_2014_RGB_602500_646600.tif'.\n"
+     ]
+    }
+   ],
+   "source": [
+    "file_path = pooch.retrieve(\n",
+    "    url=\"doi:10.5281/zenodo.5494629/Sep_2014_RGB_602500_646600.tif\",\n",
+    "    known_hash=\"md5:77a3b57f5f5946504ec520d1e793f250\",\n",
+    "    path='.',\n",
+    "    fname='Sep_2014_RGB_602500_646600.tif'\n",
+    ")"
+   ],
+   "metadata": {
+    "collapsed": false
+   }
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "Then we use `load_dataset` from `scivision.io`. This will return a `intake.catalog.local.YAMLFileCatalog` with the information of the dataset."
+   ],
+   "metadata": {
+    "collapsed": false
+   }
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 10,
    "outputs": [],
    "source": [
-    "cat = load_dataset(target_datasource.url.item()) \n",
-    "download_zenodo_files_for_entry(cat.sepilok_rgb, force_download=False)\n",
+    "cat = load_dataset(target_datasource.url.item())\n",
     "dataset = cat.sepilok_rgb().to_dask()"
-   ]
+   ],
+   "metadata": {
+    "collapsed": false
+   }
   },
   {
    "attachments": {},